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gatk-3.8/protected/java/test/org/broadinstitute/sting/gatk/walkers
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Mark DePristo 3144eae51c UnifiedGenotyper bugfix: don't create haplotypes with 0 bases 
-- The PairHMM no longer allows us to create haplotypes with 0 bases.  The UG indel caller used to create such haplotypes.  Now we assign -Double.MAX_VALUE likelihoods to such haplotypes.
-- Add integration test to cover this case, along with private/testdata BAM
-- [Fixes #47523579]
 		2013-04-13 14:57:55 -04:00
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annotator Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
beagle Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
bqsr Updating BQSR RecalibrationEngine to work correctly with empty BQSR tables. 2013-04-11 16:27:59 -04:00
compression/reducereads Updated AssessReducedQuals and applied it systematically to all ReduceReads integration tests. 2013-03-31 00:27:14 -04:00
diagnostics walker to calculate per base coverage distribution 2013-02-07 16:33:05 -05:00
diffengine Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs) 2013-03-12 10:57:14 -04:00
fasta Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
filters Don't allow users to specify keys and IDs that contain angle brackets or equals signs (not allowed in VCF spec). 2013-04-05 00:52:32 -04:00
genotyper UnifiedGenotyper bugfix: don't create haplotypes with 0 bases 2013-04-13 14:57:55 -04:00
haplotypecaller Updating java 7 md5's to java 6 md5's 2013-04-13 08:21:48 -04:00
indels Fixed IndelRealigner reference length bug (GSA-774) 2013-02-19 16:00:36 -05:00
phasing Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
validation MathUtils.randomSubset() now uses Collections.shuffle() (indirectly, through the other methods 2013-03-29 14:52:10 -04:00
varianteval Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00
variantrecalibration Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
variantutils Using --keepOriginalAC in SelectVariants was causing it to emit bad VCFs 2013-04-05 00:53:28 -04:00